[gmx-users] meaning of minus potential and buried surface area

ahmet yıldırım ahmedo047 at gmail.com
Wed Sep 21 20:50:31 CEST 2011

Dear users,

1.) During the simulation the mean potential energy is minus (-) value. What
does this mean? Why minus?
2.) let's say, Interface/Buried Surace Area (ISA) between protein and ligand
was calculated and hydrophobic ISA obtained greater than hydrophilic ISA.
What does this mean?

No one is my special advisor but If you help me, I will be happy.

Thanks in advance

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